The coloring on the cap ships haven't changed, just the tile size (also I dropped the "rivets" from the cap texture, they ended up being more problematic than good) The caps and fighters are a different shades of blue, some of the differences is from the base hull texture is different, caps have that tile.
Also the easiest way to fix the capships is just to downsize the tile texture. A lot easier than re-uvmapping everything UGH
Edit: Fixing this won't be a major problem. Resize the tiling down 50% is about right and I've got a nice script that does everything. Unfortunately my computer is so bloody slow